Australian Tree Hollow Raw sequence reads

Cryptococcosis is a severe fungal infection caused by members of the Cryptococcus gattii and C. neoformans species complexes. Especially, the C. gattii species complex has a strong environmental association with eucalypt hollows (particularly Eucalyptus camaldulensis), which may present a source of infection. It remains unclear whether a specific mycobiome is required to support its environmental growth. Conventional detection of environmental Cryptococcus spp. involves culture on differential media, such as Guizotia abyssinica seed agar. Next generation sequencing (NGS) based culture-independent identification aids in contextualising these species in the environmental mycobiome. Samples from 23 tree hollows from NSW, Australia, were subjected to both, culture- and amplicon-based metagenomic analysis, to characterise the mycobiome and assess for relationships between Cryptococcus spp. and other fungal genera. The most abundant genera detected were Coniochaeta, Aspergillus and Penicillium; all are commonly isolated from decaying wood. There was no correlation between the presence of Cryptococcus spp. in a tree hollow and the presence of any other fungal genus. Some differences in the abundance of numerous taxa were noted in a differential heat tree comparing samples with or without Cryptococcus spp. NGS reads. The study expanded the known environmental niche of the C. gattii and C. neoformans species complexes in Australia with their confirmed detections from five tree species. Discrepancies between the detection of Cryptococcus spp. using culture or NGS suggest that neither is superior and that these methodologies are complimentary. The inherent biases of amplicon-based metagenomics requires, cautious interpretation of data taking into account their biological relevance.